Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate 3608118 Dshi_1523 glucose sorbosone dehydrogenase (RefSeq)
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__Dino:3608118 Length = 369 Score = 155 bits (391), Expect = 2e-42 Identities = 114/351 (32%), Positives = 166/351 (47%), Gaps = 40/351 (11%) Query: 21 LRVEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFR-EGRLSTYAELP-VYHRGESGLL 78 + V+E+V L+ PWA FLP+GG+LI ER G + R +G + + LP + G+ GLL Sbjct: 31 VEVKEIVRDLDEPWAFGFLPEGGVLITERGGALLHIRPDGTRTEVSGLPRIAVGGQGGLL 90 Query: 79 GLALHPRFPEA-PYVYAYRTVAEGGLRNQVVRLRHLGERGVLD--RVVLDGIPARPHGLH 135 L + F + V++Y G V R + L+ R + G H Sbjct: 91 DLLIPADFAQTREVVFSYSRPQARGAGTAVAVGRFSADGRALENTRTIFAMEEGTRGGRH 150 Query: 136 SGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARPE 195 G RI G DG LYVT G+ + + AQ+LA G ++R+ +G NPF G GA+PE Sbjct: 151 FGSRIVEGRDGFLYVTIGDRGDDDSAQNLAIESGSVIRIARDGGIPTSNPFTGTEGAQPE 210 Query: 196 VYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRV------- 248 ++S GHRNPQG A + G L+ EHG G DE+N + G NYGWP + Sbjct: 211 IWSYGHRNPQGAALDLQ-GNLWVVEHG-----ARGGDEINRVEMGANYGWPVISYGRHYS 264 Query: 249 ---VGRGN-DPRYRDPLYFWPQGFPPGNLAFF--------RGDLYVAGLRGQALLRLVLE 296 +G G P P +FW P + + GD +V L+ L RL Sbjct: 265 GLRIGEGTAKPGMEQPAHFWDPSIAPSGMMIYSGALWPEWEGDFFVGSLKFGYLSRL--- 321 Query: 297 GERGRWRVLRVETALSG--FGRLREVQVGPDGALYVTTSNRDGRGQVRPGD 345 E G + E ++G RLR+V+ GPDGA++ + ++ P + Sbjct: 322 -EAGSF----AEEEITGDTTARLRDVREGPDGAIWFLSVGNGALYRMSPAE 367 Lambda K H 0.322 0.146 0.460 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 489 Number of extensions: 31 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 352 Length of database: 369 Length adjustment: 29 Effective length of query: 323 Effective length of database: 340 Effective search space: 109820 Effective search space used: 109820 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory